tbuckley/cabot-search huggingface dataset:
RUNX1 loss renders hematopoietic and leukemic cells dependent on IL-3 and sensitive to JAK inhibition
Authors: Amy C. Fan, Yusuke Nakauchi, Lawrence Bai, Armon Azizi, Kevin A. Nuno, Feifei Zhao, Thomas Köhnke, Daiki Karigane, David Cruz-Hernandez, Andreas Reinisch, Purvesh Khatri, Ravindra Majeti
Journal: Journal of Clinical Investigation (2023)

Disease-initiating mutations in the transcription factor RUNX1 occur as germline and somatic events that cause leukemias with particularly poor prognosis. However, the role of RUNX1 in leukemogenesis is not fully understood, and effective therapies for RUNX1-mutant leukemias remain elusive. Here, we used primary patient samples and a RUNX1-KO model in primary human hematopoietic cells to investigate how RUNX1 loss contributes to leukemic progression and to identify targetable vulnerabilities. Surprisingly, we found that RUNX1 loss decreased proliferative capacity and stem cell function. However, RUNX1-deficient cells selectively upregulated the IL-3 receptor. Exposure to IL-3, but not other JAK/STAT cytokines, rescued RUNX1-KO proliferative and competitive defects. Further, we demonstrated that RUNX1 loss repressed JAK/STAT signaling and rendered RUNX1-deficient cells sensitive to JAK inhibitors. Our study identifies a dependency of RUNX1-mutant leukemias on IL-3/JAK/STAT signaling, which may enable targeting of these aggressive blood cancers with existing agents.
Rescue of alveolar wall liquid secretion blocks fatal lung injury due to influenza-staphylococcal coinfection
Authors: Stephanie Tang, Ana Cassandra De Jesus, Deebly Chavez, Sayahi Suthakaran, Sarah K.L. Moore, Keshon Suthakaran, Sonya Homami, Raveen Rathnasinghe, Alison J. May, Michael Schotsaert, Clemente J. Britto, Jahar Bhattacharya, Jaime L. Hook
Journal: Journal of Clinical Investigation (2023)

Secondary lung infection by inhaled Staphylococcus aureus (SA) is a common and lethal event in individuals infected with influenza A virus (IAV). How IAV disrupts host defense to promote SA infection in lung alveoli, where fatal lung injury occurs, is not known. We addressed this issue using the first real-time determinations of alveolar responses to IAV in live, intact, perfused lungs. Our findings show IAV infection blocked defensive alveolar wall liquid (AWL) secretion and induced airspace liquid absorption, thereby reversing normal alveolar liquid dynamics and inhibiting alveolar clearance of inhaled SA. Loss of AWL secretion resulted from inhibition of the cystic fibrosis transmembrane conductance regulator (CFTR) ion channel in the alveolar epithelium, and airspace liquid absorption was caused by stimulation of the alveolar epithelial Na+ channel (ENaC). Loss of AWL secretion promoted alveolar stabilization of inhaled SA, but rescue of AWL secretion protected against alveolar SA stabilization and fatal SA-induced lung injury in IAV-infected mice. These findings reveal a central role for AWL secretion in alveolar defense against inhaled SA and identify AWL inhibition as a critical mechanism of IAV lung pathogenesis. AWL rescue may represent a new therapeutic approach for IAV-SA coinfection.
NLRP12 downregulates the Wnt/β-catenin pathway via interaction with STK38 to suppress colorectal cancer
Authors: Shahanshah Khan, Youn-Tae Kwak, Lan Peng, Shuiqing Hu, Brandi L. Cantarel, Cheryl M. Lewis, Yunpeng Gao, Ram S. Mani, Thirumala-Devi Kanneganti, Hasan Zaki
Journal: Journal of Clinical Investigation (2023)

Colorectal cancer (CRC) at advanced stages is rarely curable, underscoring the importance of exploring the mechanism of CRC progression and invasion. NOD-like receptor family member NLRP12 was shown to suppress colorectal tumorigenesis, but the precise mechanism was unknown. Here, we demonstrate that invasive adenocarcinoma development in Nlrp12-deficient mice is associated with elevated expression of genes involved in proliferation, matrix degradation, and epithelial-mesenchymal transition. Signaling pathway analysis revealed higher activation of the Wnt/β-catenin pathway, but not NF-κB and MAPK pathways, in the Nlrp12-deficient tumors. Using Nlrp12-conditional knockout mice, we revealed that NLRP12 downregulates β-catenin activation in intestinal epithelial cells, thereby suppressing colorectal tumorigenesis. Consistent with this, Nlrp12-deficient intestinal organoids and CRC cells showed increased proliferation, accompanied by higher activation of β-catenin in vitro. With proteomic studies, we identified STK38 as an interacting partner of NLRP12 involved in the inhibition of phosphorylation of GSK3β, leading to the degradation of β-catenin. Consistently, the expression of NLRP12 was significantly reduced, while p-GSK3β and β-catenin were upregulated in mouse and human colorectal tumor tissues. In summary, NLRP12 is a potent negative regulator of the Wnt/β-catenin pathway, and the NLRP12/STK38/GSK3β signaling axis could be a promising therapeutic target for CRC.
Helen Salisbury: Everyone benefits from continuity of care
Authors: Helen Salisbury
Journal: BMJ (2023)

Helen Salisbury: Everyone benefits from continuity of care Helen Salisbury GP Triage, signposting, and care navigation are buzz words that crop up frequently in discussions about the future of general practice.They form part of NHS England's vision of a leaner, cheaper service, in which simple health problems are attended to by someone with just enough skills and training for that task, leaving doctors free to concentrate on complicated cases that definitely need all that expensive training and professional expertise.5
Immune regulatory networks coordinated by glycans and glycan-binding proteins in autoimmunity and infection
Authors: Salomé S. Pinho, Inês Alves, Joana Gaifem, Gabriel A. Rabinovich
Journal: Cellular and Molecular Immunology (2023)

Abstract The immune system is coordinated by an intricate network of stimulatory and inhibitory circuits that regulate host responses against endogenous and exogenous insults. Disruption of these safeguard and homeostatic mechanisms can lead to unpredictable inflammatory and autoimmune responses, whereas deficiency of immune stimulatory pathways may orchestrate immunosuppressive programs that contribute to perpetuate chronic infections, but also influence cancer development and progression. Glycans have emerged as essential components of homeostatic circuits, acting as fine-tuners of immunological responses and potential molecular targets for manipulation of immune tolerance and activation in a wide range of pathologic settings. Cell surface glycans, present in cells, tissues and the extracellular matrix, have been proposed to serve as “self-associated molecular patterns” that store structurally relevant biological data. The responsibility of deciphering this information relies on different families of glycan-binding proteins (including galectins, siglecs and C-type lectins) which, upon recognition of specific carbohydrate structures, can recalibrate the magnitude, nature and fate of immune responses. This process is tightly regulated by the diversity of glycan structures and the establishment of multivalent interactions on cell surface receptors and the extracellular matrix. Here we review the spatiotemporal regulation of selected glycan-modifying processes including mannosylation, complex N -glycan branching, core 2 O -glycan elongation, LacNAc extension, as well as terminal sialylation and fucosylation. Moreover, we illustrate examples that highlight the contribution of these processes to the control of immune responses and their integration with canonical tolerogenic pathways. Finally, we discuss the power of glycans and glycan-binding proteins as a source of immunomodulatory signals that could be leveraged for the treatment of autoimmune inflammation and chronic infection.
BamQuery: a proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens
Authors: Maria Virginia Ruiz Cuevas, Marie-Pierre Hardy, Jean-David Larouche, Anca Apavaloaei, Eralda Kina, Krystel Vincent, Patrick Gendron, Jean-Philippe Laverdure, Chantal Durette, Pierre Thibault, Sébastien Lemieux, Claude Perreault, Grégory Ehx
Journal: Genome biology (2023)

Abstract MHC-I-associated peptides deriving from non-coding genomic regions and mutations can generate tumor-specific antigens, including neoantigens. Quantifying tumor-specific antigens’ RNA expression in malignant and benign tissues is critical for discriminating actionable targets. We present BamQuery, a tool attributing an exhaustive RNA expression to MHC-I-associated peptides of any origin from bulk and single-cell RNA-sequencing data. We show that many cryptic and mutated tumor-specific antigens can derive from multiple discrete genomic regions, abundantly expressed in normal tissues. BamQuery can also be used to predict MHC-I-associated peptides immunogenicity and identify actionable tumor-specific antigens de novo.
Ian Magrath, MD: In Memoriam (1944–2023)
Authors: Kishor Bhatia
Journal: Cancer Research (2023)

Obituary| August 15 2023 Ian Magrath, MD: In Memoriam (1944–2023) Kishor Bhatia 0000-0002-5319-7957 Kishor Bhatia * *Corresponding Author: Kishor Bhatia, Lantern Pharma, 1920 McKinney Avenue, 7th Floor, Dallas, TX 75201. E-mail: kishor@lanternpharma.com Search for other works by this author on: This Site PubMed Google Scholar Author & Article Information *Corresponding Author: Kishor Bhatia, Lantern Pharma, 1920 McKinney Avenue, 7th Floor, Dallas, TX 75201. E-mail: Cancer Res 2023;83:2635–6 Online ISSN: 1538-7445 Print ISSN: 0008-5472 ©2023 American Association for Cancer Research2023American Association for Cancer Research Cancer Res (2023) 83 (16): 2635–2636. https://doi.org/10.1158/0008-5472.CAN-23-2078 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Tools Icon Tools Get Permissions Cite Icon Cite Search Site Article Versions Icon Versions Version of Record August 15 2023 Citation Kishor Bhatia; Ian Magrath, MD: In Memoriam (1944–2023). Cancer Res 15 August 2023; 83 (16): 2635–2636. https://doi.org/10.1158/0008-5472.CAN-23-2078 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest Search Advanced Search International cooperation and collaboration in health, including disease surveillance, prevention, control, treatment, and management, have been exemplified by work on infectious diseases for several decades. Only recently have efforts to develop sustaining partnerships for global oncology come to the forefront of governmental and nongovernmental organizations. Ian Magrath championed this cause for cancer treatment and research since the beginning of his career. Sadly, the global cancer community lost this visionary on March 14, 2023. Ian Magrath was born in 1944 in the United Kingdom. He completed his medical education at the University of London and received further training at Charing Cross Hospital Medical School with Dr. Kenneth Bagshawe. It was during this time that his interest and future career path in medical oncology began to take form. Ian became interested in a tumor type that was identified by the British surgeon Dr. Dennis Burkitt in Africa. This tumor, named Burkitt's lymphoma,... You do not currently have access to this content.
Regulation of CD8+ T memory and exhaustion by the mTOR signals
Authors: Yao Chen, Ziyang Xu, Hongxiang Sun, Xinxing Ouyang, Yuheng Han, Haihui Yu, Ningbo Wu, Yiting Xie, Bing Su
Journal: Cellular and Molecular Immunology (2023)

Abstract CD8 + T cells are the key executioners of the adaptive immune arm, which mediates antitumor and antiviral immunity. Naïve CD8 + T cells develop in the thymus and are quickly activated in the periphery after encountering a cognate antigen, which induces these cells to proliferate and differentiate into effector cells that fight the initial infection. Simultaneously, a fraction of these cells become long-lived memory CD8 + T cells that combat future infections. Notably, the generation and maintenance of memory cells is profoundly affected by various in vivo conditions, such as the mode of primary activation (e.g., acute vs. chronic immunization) or fluctuations in host metabolic, inflammatory, or aging factors. Therefore, many T cells may be lost or become exhausted and no longer functional. Complicated intracellular signaling pathways, transcription factors, epigenetic modifications, and metabolic processes are involved in this process. Therefore, understanding the cellular and molecular basis for the generation and fate of memory and exhausted CD8 + cells is central for harnessing cellular immunity. In this review, we focus on mammalian target of rapamycin (mTOR), particularly signaling mediated by mTOR complex (mTORC) 2 in memory and exhausted CD8 + T cells at the molecular level.
MAVS-loaded unanchored Lys63-linked polyubiquitin chains activate the RIG-I-MAVS signaling cascade
Authors: Feng Liu, Wanxin Zhuang, Bin Song, Yuan Yang, Junqi Liu, Yi Zheng, Bingyu Liu, Jie Zheng, Wei Zhao, Chengjiang Gao
Journal: Cellular and Molecular Immunology (2023)
Abstract B003: Increasing branched-chain amino acid metabolism reduces clear cell renal cell carcinoma growth
Authors: Nathan J. Coffey, Romain Riscal, Nicolas Skuli, Nicholas P. Lesner, Michael Noji, Christine Jiang, Laura C. Kim, Xu Han, Megan C. Blair, Brian Keith, Zoltan Arany, M. Celeste Simon
Journal: Cancer Research (2023)

Abstract North America has the highest incidence of renal cancer in the world with the most common subtype being clear cell renal cell carcinoma (ccRCC). Metabolic dysfunction is a hallmark of ccRCC based on molecular analysis and its clear cell histologic appearance due to significant cytoplasmic accumulation of lipid droplets and glycogen. Using publicly available RNA-Seq and proteomic datasets, we identified reduced expression of branched-chain amino acid (BCAA) enzymes BCAA transaminase 2 (BCAT2) and the branched-chain ketoacid dehydrogenase complex (BCKDH) in ccRCC compared to healthy kidney tissue. We validated these results by confirming that BCAT2 and the BCKDH complex are decreased at the mRNA and protein level in ccRCC tumors and cell lines compared to pair-matched normal adjacent kidney tissue. The reduced expression of the BCKDH complex was reinforced at the genome level by copy number loss of BCKDH subunits DBT and BCKDHB, underscoring the selection for suppression of this pathway. Metabolomics analysis then showed that the abundance of BCAAs were decreased in ccRCC tumors. Additionally, public datasets revealed that ccRCC patients presenting low mRNA expression of any of the four BCKDH subunits DBT, BCKDHB, BCKDHA, and DLD have a worse overall survival compared to patients with higher expression. To test if reactivating the BCAA pathway would impact ccRCC growth, I inhibited BCKDK, a kinase that inactivates the BCKDH complex, pharmacologically with BT2 and genetically with shRNA. Multiple ccRCC cell lines demonstrated reduced proliferation due to apoptosis after being treated with shRNA targeting BCKDK. Cell viability could be rescued by the antioxidant N-acetyl cysteine, suggesting loss of BCKDK increased the production of reactive oxygen species (ROS). Flow cytometry showed that knocking down BCKDK increases cellular ROS. Our data reveal that BCAA catabolism is decreased in ccRCC and reactivating the pathway reduces ccRCC growth in vitro by inducing apoptosis through increased production of ROS. This suggests that BCKDK could be a therapeutic target in ccRCC. Citation Format: Nathan J. Coffey, Romain Riscal, Nicolas Skuli, Nicholas P. Lesner, Michael Noji, Christine Jiang, Laura C. Kim, Xu Han, Megan C. Blair, Brian Keith, Zoltan Arany, M. Celeste Simon. Increasing branched-chain amino acid metabolism reduces clear cell renal cell carcinoma growth [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr B003.
Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture
Authors: Jennifer R. S. Meadows, Jeffrey M. Kidd, Guo-Dong Wang, Heidi G. Parker, Peter Z. Schall, Matteo Bianchi, Matthew J. Christmas, Katia Bougiouri, Reuben M. Buckley, Christophe Hitte, Anthony K. Nguyen, Chao Wang, Vidhya Jagannathan, Julia E. Niskanen, Laurent A. F. Frantz, Meharji Arumilli, Sruthi Hundi, Kerstin Lindblad-Toh, Catarina Ginja, Kadek Karang Agustina, Catherine André, Adam R. Boyko, Brian W. Davis, Michaela Drögemüller, Xin-Yao Feng, Konstantinos Gkagkavouzis, Giorgos Iliopoulos, Alexander C. Harris, Marjo K. Hytönen, Daniela C. Kalthoff, Yan-Hu Liu, Petros Lymberakis, Nikolaos Poulakakis, Ana Elisabete Pires, Fernando Racimo, Fabian Ramos-Almodovar, Peter Savolainen, Semina Venetsani, Imke Tammen, Alexandros Triantafyllidis, Bridgett vonHoldt, Robert K. Wayne, Greger Larson, Frank W. Nicholas, Hannes Lohi, Tosso Leeb, Ya-Ping Zhang, Elaine A. Ostrander
Journal: Genome biology (2023)

The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 × data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function.
Abstract B028: Tipifarnib synergizes with axitinib in renal cell carcinoma models
Authors: Jovylyn Gatchalian, Linda Kessler, Hetika Vora Patel, Stacia Chan, Francis Burrows, Shivani Malik
Journal: Cancer Research (2023)

Abstract Clear cell renal cell carcinoma (ccRCC) is a highly vascularized tumor type, primarily due to loss of the Von Hippel-Lindau (VHL) gene that stabilizes hypoxia-inducible factor alpha proteins (HIF1α and HIF2a), primary drivers of the angiogenic response in this cell type. This includes production of angiogenic factors, such as VEGFA, which promotes the formation of blood vessels that provide tumors oxygen, nutrients, and growth factors. Anti-angiogenic tyrosine kinase inhibitors (TKIs) such as the VEGFR1/2/3 inhibitor axitinib have demonstrated therapeutic benefit in RCC patients by exploiting the critical dependency of RCC tumors on their vasculature. However, resistance to TKIs is commonly observed, leading to clinical relapse. Here, we report that the farnesyltransferase inhibitor (FTI), tipifarnib synergizes with axitinib, resulting in tumor regressions in the VHL-mutant RCC cell line-derived xenograft (CDX) models, 786-O and A498, and stasis in VHL-wild type Caki1 CDX and KI-9310 PDX models, despite the modest antitumor activity of either drug as monotherapy. To investigate the mechanism underlying this synergism, we performed immunohistochemical analysis of angiogenic markers in 786-O tumors treated with tipifarnib, axitinib, or the combination. Consistent with its mechanism of action, axitinib alone decreased angiogenesis compared to vehicle, which was evident as reduced expression of endothelial cell (EC) markers in the tumors. The combination of tipifarnib and axitinib, however, led to a further two-fold reduction in EC staining, suggesting that tipifarnib is enhancing the anti-angiogenic effect of axitinib. Further in vitro and in vivo studies are underway to establish the scope and mechanistic underpinnings of the axitinib-tipifarnib effects in RCC. Citation Format: Jovylyn Gatchalian, Linda Kessler, Hetika Vora Patel, Stacia Chan, Francis Burrows, Shivani Malik. Tipifarnib synergizes with axitinib in renal cell carcinoma models [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr B028.
Abstract IA007: A novel strategy to trigger ferroptosis in kidney cancer
Authors: Mei Yee Koh
Journal: Cancer Research (2023)

Abstract Clear cell renal cell carcinoma (ccRCC), the most common form of kidney cancer, is typically initiated by inactivation of the von Hippel Lindau (VHL) gene resulting in constitutive activation of the hypoxia inducible factors, HIF-1α and HIF-2α. VHL loss and HIF activation promote lipid accumulation that increases the sensitivity of ccRCC cells to ferroptosis. Here, we reveal Iron Sulfur Cluster Assembly 2 (ISCA2) as a novel molecular target whose inhibition decreases HIF-1/2α levels and induces ferroptosis specifically in VHL-deficient cells. ISCA2 is a component of the late mitochondrial Iron Sulfur Cluster (L-ISC) assembly complex and ISCA2 inhibition either pharmacologically or using siRNA triggers the iron starvation response, resulting in iron/metals overload and death via ferroptosis. ISCA2 inhibition also decreases HIF-2α protein levels by blocking iron-responsive element (IRE)-dependent translation, and at higher concentrations, also decreases HIF-1α translation through unknown mechanisms. Strikingly, pharmacological inhibition of ISCA2 using a novel, orally available ISCA2 inhibitor significantly reduced ccRCC xenograft growth in vivo, decreased HIF-α levels and increased lipid peroxidation, suggesting increased ferroptosis in vivo. Thus, the targeting of ISCA2 may be a promising therapeutic strategy to inhibit HIF-1/2α and to induce ferroptosis in pVHL deficient cells. Citation Format: Mei Yee Koh. A novel strategy to trigger ferroptosis in kidney cancer [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr IA007.
Abstract IA020: Exploiting cholesterol metabolism for treatment resistant ccRCC patients
Authors: M. Celeste Simon
Journal: Cancer Research (2023)

Abstract Clear cell renal cell carcinoma (ccRCC) is characterized by large intracellular lipid droplets (LDs) comprised primarily of free and esterified cholesterol molecules; however, the functional significance of cholesterol accumulation in ccRCC cells was unknown. We demonstrated that, surprisingly, genes encoding cholesterol biosynthetic pathway enzymes are strongly repressed in ccRCC cells, making them auxotrophic for exogenous cholesterol. Intriguingly, Mendelian randomization analyses of over 31,000 human genomes indicate a causal link between elevated serum levels of high-density lipoprotein (HDL) cholesterol and ccRCC risk. Depriving ccRCC cells of either cholesterol or HDL compromises proliferation and survival in vitro and ccRCC tumor growth in vivo; in contrast, elevated dietary cholesterol promotes tumor growth. We showed that Scavenger Receptor B1 (SCARB1) is uniquely required for cholesterol import by ccRCC cells, and inhibiting SCARB1 expression or activity is sufficient to cause ccRCC cell cycle arrest and apoptosis accompanied by elevated intracellular reactive oxygen species (ROS) levels and decreased PI3K/AKT signaling. Collectively, our data reveal a previously unrecognized cholesterol dependency in ccRCC and implicate SCARB1 as a therapeutic target that may contribute to novel strategies for treating kidney cancer. Citation Format: M. Celeste Simon. Exploiting cholesterol metabolism for treatment resistant ccRCC patients [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr IA020.